"It's a disgrace. This was a managed fishery, the Government for illogical but emotive reasons changed the rules," he said.

The ship's former operator Seafish Tasmania sold the vessel after the rejected applications and is now taking legal action against the Federal Government.

The company's managing director Joe Pirello says 50 job opportunities have been lost, along with $25 million annually.

"It's a lost opportunity, it's quite sad to see that one of the better vessels in the world was available to us to sustainably fish our resource and we never got a chance to actually bring that to a head," he said.

In a statement, Environment Minister Tony Burke says the Government makes no apology for not taking risks when it comes to protecting oceans.

The ship's next destination is unknown but the Seafish thinks it could be heading to the Pacific under a new name.